PomBase GTF file

A script to convert pombase gff3 file into GFT format compatible with transvar.

Requirements for running using docker

You need to have docker installed. Then simply run: bash run_with_docker.sh

The output gtf file will be at data/pombase_genome.gtf.

What it does:

• Downloads some files from pombase (see get_data.sh).
• Uses bioconvert to convert from gff3 to GFT.
• Further processes the GFT file to be compatible with transvar. The code uses the python installation of the container to run the script scripts/pombasegtf_to_ensemblgtf.py.

Requirements for running locally

Install python dependencies and activate virtual env:

poetry install
poetry shell

See the file run_locally.sh, which downloads and installs several dependencies if not present:

• samtools
• htslib

You can install them with brew or apt otherwise

# If you have linux and you want to install them globally
sudo apt install -y samtools tabix gffread

# Installing globally in mac
brew install htslib samtools gffread

Then runs bioconvert as well as the python script.